Desmond Tutorial

Preparing a Desmond simulation with the System Builder
Setting Up Membrane Systems
— my_setup.csb. This is the command file, which can be hand‐edited for custom
setup cases. For detailed documentation of the .csb file see the Schrödinger Desmond
User Manual listed in “Documentation Resources” on page 97.
And a single output file (besides a log file):
— my_setup-out.cms. This is the Maestro structure file of the entire simulation
system including OPLS‐AA force field parameters. For details on the .cms file see
the Schrödinger Desmond User Manual listed in “Documentation Resources” on
page 97.
2. Execute the following command at the command line:
$ $SCHRODINGER/run $SCHRODINGER/utilities/system_builder
my_setup.csb
where my_setup is the file name given to “Write”.
Setting Up Membrane Systems
The Membrane tab as shown in Figure 4.4 can be used to embed a membrane protein structure
in a membrane bilayer. In this procedure a template consisting of an equilibrated
membrane—including the accompanying water—is used to generate a large enough
region to encompass the protein. Using the Membrane tab, you can position the protein
within the membrane using a semi‐automated procedure.
Figure 4.4 Membrane setup in the System Builder
As a real‐life example we can consider the calcium ATPase protein, 1su4. Follow the procedure
below to prepare this protein for membrane simulation in Desmond.
To setup the 1su4 membrane protein system for Desmond simulation:
1. Open the Protein Preparation Wizard by selecting Workflows > Protein Preparation
Wizard. Type “1su4” in the PDB field and click the Import button as shown in
Figure 4.5.
2. When the structure appears in the MaestroWorkspace, set the preprocessing options
as shown in Figure 4.5; do not delete the crystal waters as they are integral to the pro‐
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